All File Changes

v255_preview2 to v255_base (2011-08-02 to 2011-08-08) v255

• java/src/edu/ucsc/genome/qa/cgiCheck/HGGeneCheck.java
  • lines changed 13, context: html, text, full: html, text
    Made HgConf.java recognize included files and improved error handling in HGGeneCheck.java.
• java/src/edu/ucsc/genome/qa/lib/HgConf.java
  • lines changed 36, context: html, text, full: html, text
    Made HgConf.java recognize included files and improved error handling in HGGeneCheck.java.
• src/README
  • lines changed 2, context: html, text, full: html, text
    Clarifying licensing part of README a bit.
• src/hg/encode/DAFs/2.0/caltechMm9ChipSample.ddf
  • lines changed 9, context: html, text, full: html, text
    Updated caltech Tfbs daf to match what metadata and experiment variable the lab wanted to track. Provided sample DDF. Updated the CV to have differentiation time course registered under treatment. Also add new control term to match to differing readLength of experiments.
• src/hg/encode/DAFs/2.0/caltechMm9Tfbs.daf
  • lines changed 12, context: html, text, full: html, text
    Updated caltech Tfbs daf to match what metadata and experiment variable the lab wanted to track. Provided sample DDF. Updated the CV to have differentiation time course registered under treatment. Also add new control term to match to differing readLength of experiments.
• src/hg/encode/encodeDownloadReadme/downloadsReadmeTemplate.txt
  • lines changed 3, context: html, text, full: html, text
    corrected files.txt line and removed line referencing md5sum
  • lines changed 36, context: html, text, full: html, text
    Final draft from Vanessa, Katrina and Cricket before initial push
  • lines changed 2, context: html, text, full: html, text
    Some how there was lots of extra space in that file
• src/hg/encode/encodeDownloadReadme/encodeDownloadReadme.pl
  • lines changed 58, context: html, text, full: html, text
    cleaned up code, rewrote other parts, added function to check group write permissions before trying to create file
  • lines changed 1, context: html, text, full: html, text
    put reminder to email
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 1, context: html, text, full: html, text
    Fixed the html printed for preamble to use a relative path to link to correct track configuration page, depending on if you are on hgdownload or hgdownload-test.
  • lines changed 22, context: html, text, full: html, text
    Commented out preamble.html, as this will not be used to generate an index.html page any long. Redmine #4759.
  • lines changed 36, context: html, text, full: html, text
    added functionality to check for README.txt and if not there, put it in.
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 1, context: html, text, full: html, text
    Added support for tar.gz files to be tracked in notes files.
  • lines changed 1, context: html, text, full: html, text
    repleace index.html with README.txt
• src/hg/encode/encodeMkFilesList/encodeMkFilesList
  • lines changed 513, context: html, text, full: html, text
    added in first version of encodeMkFilesList
  • lines changed 19, context: html, text, full: html, text
    fixed a bug when using a different directory, and when the md5sum.history file is broken
• src/hg/encode/encodeMkFilesList/makefile
  • lines changed 27, context: html, text, full: html, text
    added in first version of encodeMkFilesList
• src/hg/encode/encodeValidate/config/downloadsReadmeTemplate.txt
  • lines changed 45, context: html, text, full: html, text
    removed downloadstemplate from encodevalidate/config directory
• src/hg/encode/encodeValidate/config/redirectTemplateIndex.html
  • lines changed 31, context: html, text, full: html, text
    In case we want to switch to a redirect in the future, here is a template that is relational.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    added tag to show that a label was autogenerated
• src/hg/hgGateway/hgGateway.c
  • lines changed 1, context: html, text, full: html, text
    changes related to #4842
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 13, context: html, text, full: html, text
    changes related to #4842
  • lines changed 56, context: html, text, full: html, text
    add soft-reset button to hgHubConnect (#4815)
• src/hg/hgTables/hgTables.c
  • lines changed 15, context: html, text, full: html, text
    changes related to #4842
• src/hg/hgTables/mainPage.c
  • lines changed 2, context: html, text, full: html, text
    changes related to #4842
• src/hg/hgTracks/config.c
  • lines changed 6, context: html, text, full: html, text
    changes related to #4842
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    For dragScrooling fixed packed sideLabels on 1X and bound scrolling to within chrom. (redmine 4811)
  • lines changed 4, context: html, text, full: html, text
    A more complete fix for 1X scrolling with packed sideLabels being in image. There should be 2 separate images: data and side, and I had to find all cases that write to the sideLabel. doLeftLabel() functions were easy and taken care of by passing the right image pointer. But some drawItem code also wrote to side labels and this needed a global hvgSide pointer to write to.
  • lines changed 2, context: html, text, full: html, text
    fix problem where next/prev items didn't have a full context menu
  • lines changed 31, context: html, text, full: html, text
    Restricted some map items to not cover width of image but only width of label or width of item. This should make dragScroll more obvious.
  • lines changed 1, context: html, text, full: html, text
    changes related to #4842
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    A more complete fix for 1X scrolling with packed sideLabels being in image. There should be 2 separate images: data and side, and I had to find all cases that write to the sideLabel. doLeftLabel() functions were easy and taken care of by passing the right image pointer. But some drawItem code also wrote to side labels and this needed a global hvgSide pointer to write to.
• src/hg/hgTracks/imageV2.c
  • lines changed 1, context: html, text, full: html, text
    use a class to populate mouse events for area tags to slim down html
  • lines changed 5, context: html, text, full: html, text
    For dragScrooling fixed packed sideLabels on 1X and bound scrolling to within chrom. (redmine 4811)
  • lines changed 6, context: html, text, full: html, text
    Restricted some map items to not cover width of image but only width of label or width of item. This should make dragScroll more obvious.
  • lines changed 2, context: html, text, full: html, text
    Fixed dragging bug in IE.
  • lines changed 3, context: html, text, full: html, text
    In dragScroll, removed hgc link in left label on item in 'full' if that item doesn't have a name. Otherwise, what are you hgc'ing?
• src/hg/hgTracks/imageV2.h
  • lines changed 2, context: html, text, full: html, text
    Restricted some map items to not cover width of image but only width of label or width of item. This should make dragScroll more obvious.
• src/hg/hgTracks/netTrack.c
  • lines changed 2, context: html, text, full: html, text
    Restricted some map items to not cover width of image but only width of label or width of item. This should make dragScroll more obvious.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 24, context: html, text, full: html, text
    A more complete fix for 1X scrolling with packed sideLabels being in image. There should be 2 separate images: data and side, and I had to find all cases that write to the sideLabel. doLeftLabel() functions were easy and taken care of by passing the right image pointer. But some drawItem code also wrote to side labels and this needed a global hvgSide pointer to write to.
  • lines changed 7, context: html, text, full: html, text
    In dragScroll, removed hgc link in left label on item in 'full' if that item doesn't have a name. Otherwise, what are you hgc'ing?
• src/hg/hgTracks/variation.c
  • lines changed 14, context: html, text, full: html, text
    A more complete fix for 1X scrolling with packed sideLabels being in image. There should be 2 separate images: data and side, and I had to find all cases that write to the sideLabel. doLeftLabel() functions were easy and taken care of by passing the right image pointer. But some drawItem code also wrote to side labels and this needed a global hvgSide pointer to write to.
• src/hg/hgc/hgc.c
  • lines changed 15, context: html, text, full: html, text
    Added product ordering link for IKMC entries when available.
  • lines changed 15, context: html, text, full: html, text
    Added product ordering link for hgIkmc entries when corresponding bio resource available.
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 7, context: html, text, full: html, text
    added LICR RNA-seq, redmine# 3629
• src/hg/htdocs/images/grabber.cur
  • lines changed 0, context: html, text, full: html, text
    Restricted dragScroll to within the north-south boundaries and used the desired grabbing hands cursors.
• src/hg/htdocs/images/grabbing.cur
  • lines changed 0, context: html, text, full: html, text
    Restricted dragScroll to within the north-south boundaries and used the desired grabbing hands cursors.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 3, context: html, text, full: html, text
    By Greg's advice, usung chainTbl class and HGStyle.css to deal with hgTrackDb embedded 'matrix' table. (redmine 4848)
• src/hg/htdocs/style/hgHubConnect.css
  • lines changed 11, context: html, text, full: html, text
    changes related to #4842
• src/hg/inc/hubConnect.h
  • lines changed 3, context: html, text, full: html, text
    add soft-reset button to hgHubConnect (#4815)
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v255
• src/hg/js/hgTracks.js
  • lines changed 26, context: html, text, full: html, text
    add allowDragAndZoomEverywhere code (currently turned off; see redmine 4667); commented out my 1x panning test code
  • lines changed 2, context: html, text, full: html, text
    Fixed FF on Mac context menu bug (redmine 3468).
  • lines changed 13, context: html, text, full: html, text
    use a class to populate mouse events for area tags to slim down html
  • lines changed 10, context: html, text, full: html, text
    fix bugs in allowDragAndZoomEverywhere
  • lines changed 15, context: html, text, full: html, text
    For dragScrooling fixed packed sideLabels on 1X and bound scrolling to within chrom. (redmine 4811)
  • lines changed 17, context: html, text, full: html, text
    exeriment with using shift/cntrl to allow drag-and-select anywhere in the hgTracks images
  • lines changed 65, context: html, text, full: html, text
    remove some dead code
  • lines changed 16, context: html, text, full: html, text
    turn on mapIsUpdateable in Safari >= 5.1
  • lines changed 54, context: html, text, full: html, text
    Restricted dragScroll to within the north-south boundaries and used the desired grabbing hands cursors.
  • lines changed 4, context: html, text, full: html, text
    Restricted some map items to not cover width of image but only width of label or width of item. This should make dragScroll more obvious.
  • lines changed 17, context: html, text, full: html, text
    update safari related comments
  • lines changed 8, context: html, text, full: html, text
    Fixed the grabbing (closed) hand/dragMask for IE and removed the grabber (open) hand, again for IE. Setting the grabber cursor overrode the map item pointers.
• src/hg/js/jquery.imgareaselect.js
  • lines changed 11, context: html, text, full: html, text
    allow options.clickClipHeight to be a list; currently not used (see redmine 4781)
  • lines changed 2, context: html, text, full: html, text
    Fixed FF on Mac context menu bug (redmine 3468).
  • lines changed 9, context: html, text, full: html, text
    fix bugs in allowDragAndZoomEverywhere
  • lines changed 1, context: html, text, full: html, text
    exeriment with using shift/cntrl to allow drag-and-select anywhere in the hgTracks images
• src/hg/js/utils.js
  • lines changed 4, context: html, text, full: html, text
    Restricted dragScroll to within the north-south boundaries and used the desired grabbing hands cursors.
• src/hg/lib/fileUi.c
  • lines changed 5, context: html, text, full: html, text
    Converted 'parent dir' link to 'raw files view' link to the downloads dir.
  • lines changed 5, context: html, text, full: html, text
    Rearranged hgFileUi preamble as per Katrina and Vanessa.
  • lines changed 6, context: html, text, full: html, text
    Added Note/Warning for preview browser (redmine 4844).
• src/hg/lib/hVarSubst.c
  • lines changed 1, context: html, text, full: html, text
    By Greg's advice, usung chainTbl class and HGStyle.css to deal with hgTrackDb embedded 'matrix' table. (redmine 4848)
• src/hg/lib/hubConnect.c
  • lines changed 21, context: html, text, full: html, text
    add soft-reset button to hgHubConnect (#4815)
• src/hg/lib/web.c
  • lines changed 2, context: html, text, full: html, text
    changes related to #4842
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeHudsonalphaChipSeq.release3.notes
  • lines changed 3, context: html, text, full: html, text
    Added README.txt and added index.html to the deprecated files list. Also used fileSortOrder to track so that README would work well. Redmine #4558, #3953.
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeUwDnaseSeq.release5.notes.txt
  • lines changed 743, context: html, text, full: html, text
    Added release 5 notes files for track. Redmine #236.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes
  • lines changed 1, context: html, text, full: html, text
    Changed index.html to README.txt
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release1.notes
  • lines changed 1, context: html, text, full: html, text
    Changed index.html to README.txt
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibGenotype.release1.notes
  • lines changed 1, context: html, text, full: html, text
    Changed index.html to README.txt
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release2.notes
  • lines changed 1, context: html, text, full: html, text
    Changed index.html to README.txt
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunyRipSeq.release1.notes
  • lines changed 1, context: html, text, full: html, text
    Changed index.html to README.txt
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunySwitchgear.release1.notes
  • lines changed 1, context: html, text, full: html, text
    Changed index.html to README.txt
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhHistone.release2.notes
  • lines changed 1, context: html, text, full: html, text
    Changed index.html to README.txt
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes
  • lines changed 3911, context: html, text, full: html, text
    added notes for sydh tfbs and uw 5c
  • lines changed 5166, context: html, text, full: html, text
    updated sydhtfbs and uw5c notes files
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUncBsuProt.release1.notes
  • lines changed 1, context: html, text, full: html, text
    Changed index.html to README.txt
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUw5C.release1.notes
  • lines changed 84, context: html, text, full: html, text
    added notes for sydh tfbs and uw 5c
  • lines changed 5, context: html, text, full: html, text
    updated sydhtfbs and uw5c notes files
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhTfbs.release2.notes
  • lines changed 1, context: html, text, full: html, text
    mm9 track in the pushQ needs the index.html changed to README.txt
• src/hg/makeDb/doc/hg18.txt
  • lines changed 166, context: html, text, full: html, text
    Added evofoldV2 track.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 9, context: html, text, full: html, text
    Updated hgIkmc track using updated data file from IKMC.
• src/hg/makeDb/doc/mm9.txt
  • lines changed 141, context: html, text, full: html, text
    Updated IKMC track.
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes12.csh
  • lines changed 9, context: html, text, full: html, text
    MLQ #4783 (misnamed gene?): regenerated hg19's knownGene.ix{,x} because they lagged kgXref.
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 43, context: html, text, full: html, text
    Removed some code involving the affyExonTissues table, which would in effect only be run on hg18. Since this script won't be run on hg18 anymore, that code is now dead code
  • lines changed 31, context: html, text, full: html, text
    In efforts to keep Pfam jobs from overwhelming the filesystem, (1) run the Pfam jobs to use data on the scratch disk rather than hive, and (2) limit the processing to five CPUs at one time
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Track #4533 (High Seq Depth): adding wildcard pattern for tables to tablesIgnored $hg.
  • lines changed 2, context: html, text, full: html, text
    added two tables to tables ignored for NumtS track, one for hg19, one for mm9.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 48, context: html, text, full: html, text
    Updated caltech Tfbs daf to match what metadata and experiment variable the lab wanted to track. Provided sample DDF. Updated the CV to have differentiation time course registered under treatment. Also add new control term to match to differing readLength of experiments.
  • lines changed 1, context: html, text, full: html, text
    Added new protocol for BJ
  • lines changed 52, context: html, text, full: html, text
    Removing unused BJ stanzas and updating protocol name
  • lines changed 21, context: html, text, full: html, text
    Changeing priorities in the cv so that things are grouped together, added hidden in a few places, the comments in this area are very out of date. This will be another fix.
  • lines changed 140, context: html, text, full: html, text
    Adding registered cell lines
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra
  • lines changed 13, context: html, text, full: html, text
    Added expId's for validation images. Redmine #236
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Added fileSort order for new release. This will work with redirct in new README.txt. Redmine #4633, Redmine #236.
  • lines changed 156, context: html, text, full: html, text
    Organizing the include statements for easy management
  • lines changed 1, context: html, text, full: html, text
    We had pulled this data, I do not know why we still have include file
  • lines changed 14, context: html, text, full: html, text
    Removed duplication of includes brought about by incorrect merge resolution.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncodeYaleRnaSeq.new.ra
  • lines changed 75, context: html, text, full: html, text
    More files that are not used in the structure and are copies of other files in the structure.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncodeYaleRnaSeq.ra
  • lines changed 75, context: html, text, full: html, text
    More files that are not used in the structure and are copies of other files in the structure.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.new.ra
  • lines changed 1002, context: html, text, full: html, text
    More files that are not used in the structure and are copies of other files in the structure.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBuOrchid.ra
  • lines changed 1, context: html, text, full: html, text
    Taking empty column out of fileSortOrder
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlRnaSeq.html
  • lines changed 105, context: html, text, full: html, text
    This file is not being used
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 538, context: html, text, full: html, text
    Another file that is not being used right now
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExon.new.ra
  • lines changed 421, context: html, text, full: html, text
    These are all files that are no longer referenced and/or are redundant. I am removing for clarity.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExonArray.new.html
  • lines changed 87, context: html, text, full: html, text
    These are all files that are no longer referenced and/or are redundant. I am removing for clarity.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.new.ra
  • lines changed 109, context: html, text, full: html, text
    These are all files that are no longer referenced and/or are redundant. I am removing for clarity.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.new.ra
  • lines changed 300, context: html, text, full: html, text
    These are all files that are no longer referenced and/or are redundant. I am removing for clarity.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.new.ra
  • lines changed 60, context: html, text, full: html, text
    More files that are not used in the structure and are copies of other files in the structure.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
  • lines changed 1, context: html, text, full: html, text
    Added README.txt and added index.html to the deprecated files list. Also used fileSortOrder to track so that README would work well. Redmine #4558, #3953.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.new.html
  • lines changed 101, context: html, text, full: html, text
    These are all files that are no longer referenced and/or are redundant. I am removing for clarity.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.new.ra
  • lines changed 177, context: html, text, full: html, text
    More files that are not used in the structure and are copies of other files in the structure.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapabilityOld.html
  • lines changed 109, context: html, text, full: html, text
    More files that are not used in the structure and are copies of other files in the structure.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.new.ra
  • lines changed 2273, context: html, text, full: html, text
    More files that are not used in the structure and are copies of other files in the structure.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.new.ra
  • lines changed 221, context: html, text, full: html, text
    More files that are not used in the structure and are copies of other files in the structure.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.html
  • lines changed 3, context: html, text, full: html, text
    Added new release notes that include addition of validation images. Redmine #236
  • lines changed 113, context: html, text, full: html, text
    More files that are not used in the structure and are copies of other files in the structure.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.ra
  • lines changed 1, context: html, text, full: html, text
    Added fileSort order for new release. This will work with redirct in new README.txt. Redmine #4633, Redmine #236.
  • lines changed 1648, context: html, text, full: html, text
    More files that are not used in the structure and are copies of other files in the structure.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeqRelease2.html
  • lines changed 114, context: html, text, full: html, text
    More files that are not used in the structure and are copies of other files in the structure.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.new.html
  • lines changed 178, context: html, text, full: html, text
    More files that are not used in the structure and are copies of other files in the structure.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleRnaSeq.ra
  • lines changed 75, context: html, text, full: html, text
    More files that are not used in the structure and are copies of other files in the structure.
• src/hg/makeDb/trackDb/human/hg19/evoCpg.html
  • lines changed 1, context: html, text, full: html, text
    Corrected track name
• src/hg/makeDb/trackDb/human/hg19/knownGene.html
  • lines changed 1, context: html, text, full: html, text
    Fixed link to UniProt
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    added gencode to makefile
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra
  • lines changed 153, context: html, text, full: html, text
    made metadata file for gencode v3
  • lines changed 4, context: html, text, full: html, text
    removed quotes
  • lines changed 115, context: html, text, full: html, text
    this is my hand made one
  • lines changed 26, context: html, text, full: html, text
    reprinted out again
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV4.ra
  • lines changed 8, context: html, text, full: html, text
    Fixing V4 to have fileSortOrder and for the metaData to line up with the composite name
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging SUNY Switchgear on beta, redmine #169
  • lines changed 1, context: html, text, full: html, text
    staging on beta, redmine#1708
  • lines changed 2, context: html, text, full: html, text
    fixing merge conflict
  • lines changed 1, context: html, text, full: html, text
    releasing Cricket's fixes to Gencode Genes so it is Gencode Genes V4 and fixing up other things: adding expId, UCSC Accession, adding V4 to labels, adding fileSortOrder, removing dateRestricted sicne they are unrestricted data, redmine #3953 note 63
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGencodeV4.ra
  • lines changed 110, context: html, text, full: html, text
    releasing Cricket's fixes to Gencode Genes so it is Gencode Genes V4 and fixing up other things: adding expId, UCSC Accession, adding V4 to labels, adding fileSortOrder, removing dateRestricted sicne they are unrestricted data, redmine #3953 note 63
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibGenotype.ra
  • lines changed 2117, context: html, text, full: html, text
    staging on beta, redmine#1708
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunySwitchgear.ra
  • lines changed 46, context: html, text, full: html, text
    staging SUNY Switchgear on beta, redmine #169
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    releasing Cricket's fixes to Gencode Genes so it is Gencode Genes V4 and fixing up other things: adding expId, UCSC Accession, adding V4 to labels, adding fileSortOrder, removing dateRestricted sicne they are unrestricted data, redmine #3953 note 63
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGencodeV4.ra
  • lines changed 110, context: html, text, full: html, text
    releasing Cricket's fixes to Gencode Genes so it is Gencode Genes V4 and fixing up other things: adding expId, UCSC Accession, adding V4 to labels, adding fileSortOrder, removing dateRestricted sicne they are unrestricted data, redmine #3953 note 63
• src/hg/makeDb/trackDb/human/hg19/numtSeqHg19.html
  • lines changed 84, context: html, text, full: html, text
    Cleaned up html. Added hard wraps at 100 chars. Cleaned up text for grammar.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    staging SUNY Switchgear on beta, redmine #169
  • lines changed 1, context: html, text, full: html, text
    staging on beta, redmine#1708
  • lines changed 2, context: html, text, full: html, text
    Staged a leak of the fileSortOrder for this older track. See ticket 3953 item 57
  • lines changed 2, context: html, text, full: html, text
    releasing Cricket's fixes to Gencode Genes so it is Gencode Genes V4 and fixing up other things: adding expId, UCSC Accession, adding V4 to labels, adding fileSortOrder, removing dateRestricted sicne they are unrestricted data, redmine #3953 note 63
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
  • lines changed 110, context: html, text, full: html, text
    Changing the description and matrix as requested by the lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Changing the description and matrix as requested by the lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.ra
  • lines changed 3, context: html, text, full: html, text
    comment out metadata lines
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.new.ra
  • lines changed 5, context: html, text, full: html, text
    Fixing V4 to have fileSortOrder and for the metaData to line up with the composite name
  • lines changed 6, context: html, text, full: html, text
    Capitals and html file name
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.ra
  • lines changed 10, context: html, text, full: html, text
    releasing Cricket's fixes to Gencode Genes so it is Gencode Genes V4 and fixing up other things: adding expId, UCSC Accession, adding V4 to labels, adding fileSortOrder, removing dateRestricted sicne they are unrestricted data, redmine #3953 note 63
  • lines changed 6, context: html, text, full: html, text
    Cricket had forgotten to check in some changes, she did and so I am copying from .new.ra again to pick them up, redmine #3953 note 57
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.html
  • lines changed 8, context: html, text, full: html, text
    added track displays and conventions
  • lines changed 1, context: html, text, full: html, text
    QA fixes, broken link and viewUi off, Track#2234 notes#31 and #32
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
  • lines changed 1, context: html, text, full: html, text
    Turned viewUi off at request of QA
  • lines changed 1, context: html, text, full: html, text
    QA fixes, broken link and viewUi off, Track#2234 notes#31 and #32
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.new.ra
  • lines changed 106, context: html, text, full: html, text
    Staged a leak of the fileSortOrder for this older track. See ticket 3953 item 57
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra
  • lines changed 1, context: html, text, full: html, text
    Added file sort ourder with a comment
  • lines changed 1, context: html, text, full: html, text
    Staged a leak of the fileSortOrder for this older track. See ticket 3953 item 57
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.html
  • lines changed 20, context: html, text, full: html, text
    Changing the html according to jacob requests, mostly broken links, missing periods and the likesee 1709
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.html
  • lines changed 4, context: html, text, full: html, text
    Responding to ticket #169. Removed the filter in trackDb and added a clarifying sentance in .html
  • lines changed 24, context: html, text, full: html, text
    Much rewriting under advice of QA, see ticket #169
  • lines changed 1, context: html, text, full: html, text
    removing repeated words, redmine 169
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.ra
  • lines changed 10, context: html, text, full: html, text
    Responding to ticket #169. Removed the filter in trackDb and added a clarifying sentance in .html
  • lines changed 10, context: html, text, full: html, text
    Fixing the display issue that Tim found with noInherit on
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    Releasing LICR RNA-Seq, redmine# 3629
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeLicrRnaSeq.ra
  • lines changed 1666, context: html, text, full: html, text
    Releasing LICR RNA-Seq, redmine# 3629
• src/hg/makeDb/trackDb/mouse/mm9/numtSeqMm9.html
  • lines changed 62, context: html, text, full: html, text
    Cleaned up html formatting. Added hard wrap at 100 chars. Corrected grammar.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 3, context: html, text, full: html, text
    Added CalTech TFBS track, so that lab can understand the use of dimensions in for the track. Redmine #3733, note 21.
  • lines changed 4, context: html, text, full: html, text
    Merge branch 'master' into CaltechMm9DafTrial
  • lines changed 4, context: html, text, full: html, text
    Merge branch 'CaltechMm9DafTrial'
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.ra
  • lines changed 105, context: html, text, full: html, text
    Added CalTech TFBS track, so that lab can understand the use of dimensions in for the track. Redmine #3733, note 21.
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    PAR is only on chroms X and Y
• src/hg/oneShot/cartFreen/cartFreen.c
  • lines changed 148, context: html, text, full: html, text
    Making a little cart activity simulator and time measurer.
  • lines changed 10, context: html, text, full: html, text
    Seeding random number generator with pid.
  • lines changed 15, context: html, text, full: html, text
    Adding a few more things to cart activity simulator.
  • lines changed 2, context: html, text, full: html, text
    Fixing usage message order.
  • lines changed 1, context: html, text, full: html, text
    Fixed bug in output label.
  • lines changed 160, context: html, text, full: html, text
    Renaming cartFreen to cartSimNoInsert
• src/hg/oneShot/cartFreen/makefile
  • lines changed 18, context: html, text, full: html, text
    Making a little cart activity simulator and time measurer.
  • lines changed 18, context: html, text, full: html, text
    Renaming cartFreen to cartSimNoInsert
• src/hg/oneShot/cartSim/cartSim.c
  • lines changed 319, context: html, text, full: html, text
    Starting more general purpose cart simulator.
  • lines changed 9, context: html, text, full: html, text
    Finishing implementation of clone option.
  • lines changed 113, context: html, text, full: html, text
    Starting to implement cartSimulator()
  • lines changed 76, context: html, text, full: html, text
    Getting it to insert randomly now and again.
  • lines changed 48, context: html, text, full: html, text
    Implementing cgiDelay
  • lines changed 81, context: html, text, full: html, text
    Adding cleanup and engine options.
  • lines changed 2, context: html, text, full: html, text
    Removing userCount from usage message until at least it's implemented.
• src/hg/oneShot/cartSim/makefile
  • lines changed 18, context: html, text, full: html, text
    Starting more general purpose cart simulator.
• src/hg/oneShot/cartSimNoInsert/cartSimNoInsert.c
  • lines changed 163, context: html, text, full: html, text
    Renaming cartFreen to cartSimNoInsert
  • lines changed 5, context: html, text, full: html, text
    Removing stray function prototype.
• src/hg/oneShot/cartSimNoInsert/makefile
  • lines changed 18, context: html, text, full: html, text
    Renaming cartFreen to cartSimNoInsert
• src/hg/oneShot/oneShot.c
  • lines changed 34, context: html, text, full: html, text
    Removing a stray .c file.
• src/hg/txGene/txGeneValidation/compareTableSizesFromDbSnoop.py
  • lines changed 50, context: html, text, full: html, text
    Adding a script to help in the validation of UCSC Genes by comparing old and new table sizes, in old and new dbSnoop output files
• src/lib/udc.c
  • lines changed 21, context: html, text, full: html, text
    Adding some verbose logging info to udcCleanup.
  • lines changed 67, context: html, text, full: html, text
    adding 4k readAhead buffer for sparseData reduces thousands of reads down to a dozen
• src/utils/bedToClosestPoint/bedToClosestPoint.c
  • lines changed 153, context: html, text, full: html, text
    Adding new utility that is useful for associating features with closest promoter.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v255 final build

• lines changed: 26511
• files changed: 207